7. Can I just run BWA-MEM against GRCh38+ALT without post-processing? If you are not interested in hits to ALT contigs, it is okay to run BWA-MEM without post-processing. The alignments produced this way are very close to alignments against GRCh38 without ALT contigs. Nonetheless, applyin...
BWA-MEM算法记录 BWA-MEM算法记录 BWA-MEM算法整体流程如下：1 读⼊ bwt、options、reads；2 利⽤mem_chain⽣成chain；3 利⽤mem_chain_flt过滤掉部分chain；4 利⽤mem_chain2aln⽣成⽐对结果元数据。BWA采⽤seed-and-extend策略。在seed阶段，BWA取read的碱基⽚段在reference上进⾏精确匹配，并...
A gap of length k costs O + k*E (i.e. -O is for opening a zero-length gap). [1] -L INT Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best SW score minus the clipping ...
𝑗𝑈-a\log_{4}P(d_{ij})<U, BWA-MEM prefers to pair the two ends; otherwise it prefers the unpaired alignments. BWA-MEM chooses the pair(i,j)𝑖𝑗(i,j)that maximizesSijsubscript𝑆𝑖𝑗S_{ij}as the final alignments for both ends. This pairing strategy jointly considers...
bwa mem性能较好、可靠稳定,一直是WES/WGS数据分析的首选比对工具,随着技术的发展,有了越来越多的可替代方案。 1. Minimap2( https://github.com/lh3/minimap2 ) 在bwa的作者李恒的博客( https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa )《Minimap2 and the future of BWA》中写道:...
基因数据处理8之BWA_MEM小数据集处理 环境:ubuntu14.04 6G内存 参考基因:GRCH38 来源请参考【1】 1.fastq数据:SRR003161.fastq 的头20行,即5条reads 操作记录: hadoop@Master:~/cloud/adam/xubo/data/test20160310$ cat SRR003161.fastq |head -20 >SRR003161h20.fastq ...
BWA-MEM 算法比对70bp-1Mbp的输入序列。简要的说,算法主要是通过最大精确匹配作为种子比对,然后基于Smith-Waterman算法进行仿射空位罚分。 如果mate.fq文件是缺失的和选项-p并未设置。这个命令说明数据为单端测序。如果mates.fa存在,命令行假设reads.fq的第i行与mates.fq的第i行形成read对。如果-p被使用,命令行假...
thiscommandassumesthei-threadinreads.fqandthei-threadinmates.fqconstituteareadpair.If-pisused,thecommandassumesthe2i-thandthe(2i+1)-threadinreads.fqconstituteareadpair(suchinputfileissaidtobeinterleaved).Inthiscase,mates.fqisignored.Inthepaired-endmode,thememcommandwillinferthereadorientationandtheinsert...
minimap2 -t16-axmap-pb -r2k dbg.raw.fa reads.fa.gz | samtoolssort-@4 >dbg.bam samtools view -F0x900dbg.bam | wtpoa-cns -t16-d dbg.raw.fa -i - -fodbg.cns.fa #用二代数据进行纠错: bwaindexdbg.cns.fa bwa mem -t16../dbg.cns.fa sr.1.fa sr.2.fa | samtoolssort-O SAM ...
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/resources [INFO] [INFO] --- maven-scala-plugin:2.15.2:compile (default) @...